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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Structure of the FloA-NfeD dimer | |||||||||
![]() | Cryo EM map of the FloA-NfeD heterodimer | |||||||||
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![]() | small membrane protein / chapperone / lipid rafts / antibiotic resistance / staphylococcus / membrane microdomains / MEMBRANE PROTEIN | |||||||||
Function / homology | Flotillin-like protein FloA / Flotillin-like protein FloA / NfeD-like, C-terminal domain / NfeD-like C-terminal, partner-binding / membrane raft / Nucleic acid-binding, OB-fold / plasma membrane / NfeD-like C-terminal domain-containing protein / Flotillin-like protein FloA![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.8 Å | |||||||||
![]() | Ukleja M / Kricks L / Torrens G / Peschiera I / Rodrigues-Lopes I / Krupka M / Garcia Fernandez J / del Campo R / Eulalio A / Mateus A ...Ukleja M / Kricks L / Torrens G / Peschiera I / Rodrigues-Lopes I / Krupka M / Garcia Fernandez J / del Campo R / Eulalio A / Mateus A / Lopez Bravo M / Rico AI / Cava F / Lopez D | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure of the S.aureus FloA-NdeD dimer Authors: Ukleja M / Kricks L / Torrens G / Peschiera I / Rodrigues-Lopes I / Krupka M / Garcia Fernandez J / del Campo R / Eulalio A / Mateus A / Lopez Bravo M / Rico AI / Cava F / Lopez D | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.2 KB 18.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 51.1 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 20.6 MB 20.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 671.8 KB | Display | ![]() |
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Full document | ![]() | 671.4 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Cryo EM map of the FloA-NfeD heterodimer | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0108 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B
File | emd_17231_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_17231_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : FloA- NfeD dimer
Entire | Name: FloA- NfeD dimer |
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Components |
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-Supramolecule #1: FloA- NfeD dimer
Supramolecule | Name: FloA- NfeD dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: S.aureus FloA protein in complex with NfeD, forming a heterotetramer (dier of heterodimers) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 140 KDa |
-Macromolecule #1: FloA- flotilin linke protein
Macromolecule | Name: FloA- flotilin linke protein / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MFSLSFIVIA VIIIVALLIL FSFVPIGLWI SALAAGVHVG IGTLVGMRLR RVSPRKVIAP LIKAHKAGLA LTTNQLESHY LAGGNVDRVV DANIAAQRAD IDLPFERAAA IDLAGRDVLE AVQMSVNPKV IETPFIAGVA MNGIEVKAKA RITVRANIAR LVGGAGEETI ...String: MFSLSFIVIA VIIIVALLIL FSFVPIGLWI SALAAGVHVG IGTLVGMRLR RVSPRKVIAP LIKAHKAGLA LTTNQLESHY LAGGNVDRVV DANIAAQRAD IDLPFERAAA IDLAGRDVLE AVQMSVNPKV IETPFIAGVA MNGIEVKAKA RITVRANIAR LVGGAGEETI IARVGEGIVS TIGSSKHHTE VLENPDNISK TVLSKGLDSG TAFEILSIDI ADVDISKNIG ADLQTEQALA DKNIAQAKAE ERRAMAVATE QEMKARVQEM HAKVVEAESE VPLAMAEALR SGNISVKDYY NLKNIEADTG MRNAINKRTD QSDDESPEH UniProtKB: Flotillin-like protein FloA |
-Macromolecule #2: flotilin associated protein NfeD
Macromolecule | Name: flotilin associated protein NfeD / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO |
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Source (natural) | Organism: ![]() |
Sequence | String: MSYNNFLQMT TILESTAGDT WVEQVSNIIV QPIFTLILTC LTFLGFVYQL YSKKINAAGI IATLSLLILF LGFLIQGNVN MHSILIFSIG VILVVIELFV VGAVIGIIGM ILITINITTL GDNLLFMLAN VIVALILTIV EWVILVKIFN RKIPFLDKVI LKDSTNSESG ...String: MSYNNFLQMT TILESTAGDT WVEQVSNIIV QPIFTLILTC LTFLGFVYQL YSKKINAAGI IATLSLLILF LGFLIQGNVN MHSILIFSIG VILVVIELFV VGAVIGIIGM ILITINITTL GDNLLFMLAN VIVALILTIV EWVILVKIFN RKIPFLDKVI LKDSTNSESG YNSHDNRSHL VGKTAQTVTD LRPAGIIFCE NERIDAVSDG NFILRNKTVK ILEVEGTRVV VREVD UniProtKB: NfeD-like C-terminal domain-containing protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | Full lenght FloA- NfeD complex |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 19615 / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Protocol: FLEXIBLE FIT |